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Salewski J, Escobar FV, Kaminski S, von Stetten D, Keidel A, Rippers Y, Michael N, Scheerer P, Piwowarski P, Bartl F, Frankenberg-Dinkel N, Ringsdorf S, Gärtner W, Lamparter T, Mroginski MA, Hildebrandt P. Structure of the biliverdin cofactor in the Pfr state of bathy and prototypical phytochromes. J Biol Chem 2013; 288:16800-16814. [PMID: 23603902 DOI: 10.1074/jbc.m113.457531] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Phytochromes act as photoswitches between the red- and far-red absorbing parent states of phytochromes (Pr and Pfr). Plant phytochromes display an additional thermal conversion route from the physiologically active Pfr to Pr. The same reaction pattern is found in prototypical biliverdin-binding bacteriophytochromes in contrast to the reverse thermal transformation in bathy bacteriophytochromes. However, the molecular origin of the different thermal stabilities of the Pfr states in prototypical and bathy bacteriophytochromes is not known. We analyzed the structures of the chromophore binding pockets in the Pfr states of various bathy and prototypical biliverdin-binding phytochromes using a combined spectroscopic-theoretical approach. For the Pfr state of the bathy phytochrome from Pseudomonas aeruginosa, the very good agreement between calculated and experimental Raman spectra of the biliverdin cofactor is in line with important conclusions of previous crystallographic analyses, particularly the ZZEssa configuration of the chromophore and its mode of covalent attachment to the protein. The highly homogeneous chromophore conformation seems to be a unique property of the Pfr states of bathy phytochromes. This is in sharp contrast to the Pfr states of prototypical phytochromes that display conformational equilibria between two sub-states exhibiting small structural differences at the terminal methine bridges A-B and C-D. These differences may mainly root in the interactions of the cofactor with the highly conserved Asp-194 that occur via its carboxylate function in bathy phytochromes. The weaker interactions via the carbonyl function in prototypical phytochromes may lead to a higher structural flexibility of the chromophore pocket opening a reaction channel for the thermal (ZZE → ZZZ) Pfr to Pr back-conversion.
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Sarikaya H, Yilmaz M, Michael N, Miserez AR, Steinmann B, Baumgartner RW. Zurich Fabry study - prevalence of Fabry disease in young patients with first cryptogenic ischaemic stroke or TIA. Eur J Neurol 2012; 19:1421-6. [DOI: 10.1111/j.1468-1331.2012.03737.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2012] [Accepted: 03/02/2012] [Indexed: 01/30/2023]
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Mutengu LN, Kibuuka H, Millard M, Sekiziyivu A, Wakabi S, Nanyondo J, Kawooya G, Robb M, Michael N. Referral and access to care of HIV prevalent cases; experience from the early capture HIV cohort study in Kampala. Retrovirology 2012. [PMCID: PMC3441750 DOI: 10.1186/1742-4690-9-s2-o28] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Hu H, Nau M, Ehrenberg P, Chenine A, Daye Z, Wei Z, Michael N, Vahey M, Kim J, Marovich M, Ratto-Kim S. Distinct gene expression profiles associated with the susceptibility of pathogen-specific CD4+ T cells to HIV-1 infection. Retrovirology 2012. [PMCID: PMC3441412 DOI: 10.1186/1742-4690-9-s2-o46] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Pollara J, Bonsignori M, Moody M, Alam M, Liao H, Hwang K, Pickeral J, Kappes J, Ochsenbauer C, Soderberg K, Gurley TC, Kozink DM, Marshall DJ, Whitesides JF, Montefiori D, Robinson JE, Kaewkungwal J, Nitayaphan S, Pitisuttithum P, Rerks-Ngarm S, Kim J, Michael N, Tomaras G, Haynes BF, Ferrari G. Vaccine-induced ADCC-mediating antibodies target unique and overlapping envelope epitopes. Retrovirology 2012. [PMCID: PMC3441773 DOI: 10.1186/1742-4690-9-s2-o39] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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Chung A, Dugast A, Robinson H, Chan Y, Ackerman ME, Cox J, Koff W, Barouch D, Rerks-Ngarm S, Michael N, Kim J, Alter G. Vector induced skewing of antibody Fc-effector functions. Retrovirology 2012. [PMCID: PMC3442037 DOI: 10.1186/1742-4690-9-s2-p361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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Slike BM, Tassaneetrithep B, Nitayaphan S, Rono K, Sanga E, Sekiziyivu A, Stablein D, Eller L, Eller MA, Kim J, Michael N, Robb M, Marovich M. Early immune events during acute HIV infection. Retrovirology 2012. [PMCID: PMC3441840 DOI: 10.1186/1742-4690-9-s2-p181] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Franchini G, Pegu P, Gordon S, Keele B, Doster M, Guan Y, Ferrari G, Pal R, Ferrari MG, Whitney S, Hudacik L, Billings E, Rao M, Montefiori D, Venzon D, Fenizia C, Lifson J, Stablein D, Tartaglia J, Michael N, Kim J. Antibodies to the envelope protein protect macaques from SIVmac251 acquisition in an immunization regimen that mimics the RV-144 Thai trial. Retrovirology 2012. [PMCID: PMC3441518 DOI: 10.1186/1742-4690-9-s2-o2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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Kibuuka HN, Rono K, Maganga L, Millard M, Sekiziyivu A, Maboko L, Shaffer D, Valenzuela A, Michael N, Robb M. Pattern of HIV risk behavior in a cohort of high risk women in East Africa. Retrovirology 2012. [PMCID: PMC3441943 DOI: 10.1186/1742-4690-9-s2-p124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Cincotta CDM, Wieczorek LM, Barrows B, Brown B, Asher L, Michael N, Marovich M, Polonis VR. The impact of differences in viral entry and trafficking on the mechanism of HIV-1 neutralization. Retrovirology 2012. [PMCID: PMC3442047 DOI: 10.1186/1742-4690-9-s2-p58] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Wieczorek L, Rao M, Peachman K, Steers N, Marovich M, Michael N, Polonis V, Rao V. Immunogenic selection of HIV-1 MPER epitopes for improved vaccine design. Retrovirology 2012. [PMCID: PMC3441291 DOI: 10.1186/1742-4690-9-s2-p322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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Polonis V, Wieczorek L, Kalyanaraman V, Matyas G, Whitney S, Williams C, Tovanabutra S, Sanders-Buell E, Wesberry M, Ochsenbauer C, Chenine A, Rao M, Tong T, Alving C, Cheng H, Zolla-Pazner S, Michael N, VanCott T, Marovich M. Antigenicity and immunogenicity of a novel, acute HIV-1 Tanzanian subtype C gp145 envelope protein for clinical development. Retrovirology 2012. [PMCID: PMC3441268 DOI: 10.1186/1742-4690-9-s2-p323] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Zwanzger P, Zavorotnyy M, Diemer J, Ruland T, Domschke K, Christ M, Michael N, Pfleiderer B. Auditory processing in remitted major depression: a long-term follow-up investigation using 3T-fMRI. J Neural Transm (Vienna) 2012; 119:1565-73. [DOI: 10.1007/s00702-012-0871-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2011] [Accepted: 07/20/2012] [Indexed: 11/24/2022]
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Piwowarski P, Ritter E, Hofmann KP, Hildebrandt P, von Stetten D, Scheerer P, Michael N, Lamparter T, Bartl F. Light-induced activation of bacterial phytochrome Agp1 monitored by static and time-resolved FTIR spectroscopy. Chemphyschem 2010; 11:1207-14. [PMID: 20333618 DOI: 10.1002/cphc.200901008] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Phytochromes, which regulate many biological processes in plants, bacteria, and fungi, can exist in two stable states, Pr and Pfr, that can be interconverted by light, via a number of intermediates such as meta-Rc. Herein we employ FTIR spectroscopy to study the Pr-to-Pfr conversion of the bacteriophytochrome Agp1 from Agrobacterium tumefaciens. Static FTIR Pfr/Pr and meta-Rc/Pr difference spectra are disentangled in terms of cofactor and protein structural changes. Guided by DFT calculations on cofactor models, the chromophore conformational changes can be grouped into structural adjustments of the cofactor-protein interactions localized in the C-D dipyrrole moiety, that is, the photoisomerisation site, and in the A-B dipyrrole moiety including the protein attachment site. Whereas changes at the C and D rings appear to be largely completed in the meta-Rc state, the structural changes in the A-B unit occur during the transition from meta-Rc to Pfr, concomitant with the main protein structural changes, as demonstrated by static and time-resolved FTIR difference spectroscopy. We employ this technique to monitor, for the first time, the dynamics of the photocycle of phytochrome on the millisecond timescale. By extending the studies to genetically engineered protein variants of Agp1, we further demonstrate that H250 and D197 as well as the PHY domain are essential for formation of the Pfr state. Based on the IR spectroscopic and available crystallographic data we discuss the role of critical amino acid residues for the protein-cofactor interactions during the photoinduced reaction cycle.
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Scheerer P, Michael N, Park JH, Nagano S, Choe HW, Inomata K, Borucki B, Krauß N, Lamparter T. Light-Induced Conformational Changes of the Chromophore and the Protein in Phytochromes: Bacterial Phytochromes as Model Systems. Chemphyschem 2010; 11:1090-105. [DOI: 10.1002/cphc.200900913] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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Mariottini G, Morbidi F, Prattichizzo D, Vander Valk N, Michael N, Pappas G, Daniilidis K. Vision-Based Localization for Leader–Follower Formation Control. IEEE T ROBOT 2009. [DOI: 10.1109/tro.2009.2032975] [Citation(s) in RCA: 117] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Bakari M, Aboud S, Nilsson C, Francis J, Buma D, Moshiro C, Aris EA, Lyamuya E, Janabi M, Mbwana J, Mwanyika L, Stout R, Hejdeman B, Brave A, Robb M, Marovich M, Michael N, Earl P, Moss B, Wahren B, Biberfeld G, Pallangyo K, Mhalu F, Sandstrom E. P14-14 LB. A low dose of multigene, multiclade HIV DNA given intradermally induces strong and broad immune responses after boosting with heterologous HIV MVA. Retrovirology 2009. [PMCID: PMC2767919 DOI: 10.1186/1742-4690-6-s3-p403] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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Currier JR, De Souza M, Ratto-Kim S, Paris R, Nguay V, Cox J, Earl P, Moss B, Sriplienchan S, Thongcharoen P, Kim J, Robb M, Michael N, Marovich M. OA04-03. Characterization of cell-mediated immune responses generated by recombinant modified vaccinia Ankara (rMVA)-HIV-1 in a phase I vaccine trial. Retrovirology 2009. [PMCID: PMC2767548 DOI: 10.1186/1742-4690-6-s3-o27] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Zavorotnyy M, Zwanzger P, Diemer J, Christ M, Michael N, Arolt V, Pfleiderer B. Altered Auditive Processing as a Possible Trait-Marker of Major Depressive Disorder. PHARMACOPSYCHIATRY 2009. [DOI: 10.1055/s-0029-1240258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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45
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Moshtagh N, Michael N, Jadbabaie A, Daniilidis K. Vision-Based, Distributed Control Laws for Motion Coordination of Nonholonomic Robots. IEEE T ROBOT 2009. [DOI: 10.1109/tro.2009.2022439] [Citation(s) in RCA: 159] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Tollkötter M, Sörös P, Michael N, Pfleiderer B. 129. Effects of antidepressive therapy on auditory processing on auditory processing in severely depressed patients: A combined MRS and MEG study. Clin Neurophysiol 2009. [DOI: 10.1016/j.clinph.2008.07.127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Krieger A, Molina I, Oberpichler I, Michael N, Lamparter T. Spectral properties of phytochrome Agp2 from Agrobacterium tumefaciens are specifically modified by a compound of the cell extract. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2008; 93:16-22. [DOI: 10.1016/j.jphotobiol.2008.07.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2008] [Revised: 05/24/2008] [Accepted: 07/04/2008] [Indexed: 11/29/2022]
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Tollkötter M, Sörös P, Michael N, Pfleiderer B. Effects of antidepressive therapy on auditory processing on auditory processing in severely depressed patients: A combined MRS and MEG study. KLIN NEUROPHYSIOL 2008. [DOI: 10.1055/s-2008-1072923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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49
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Werth E, Michael N, Siccoli M, Bassetti C. Behaviourally induced insufficient sleep syndrome: A case series of 31 patients. Clin Neurophysiol 2008. [DOI: 10.1016/j.clinph.2007.09.105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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50
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Schumann C, Gross R, Michael N, Lamparter T, Diller R. Sub-picosecond mid-infrared spectroscopy of phytochrome Agp1 from Agrobacterium tumefaciens. Chemphyschem 2007; 8:1657-63. [PMID: 17614346 DOI: 10.1002/cphc.200700210] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The photoinduced primary reaction of the biliverdin binding phytochrome Agp1 (Agp1-BV) from Agrobacterium tumefaciens was investigated by sub-picosecond time-resolved Vis pump-IR probe spectroscopy. Three time constants of tau(1)=0.7+/-0.05 ps, tau(2)=3.3+/-0.2 ps and tau(3)=33.3+/-1.5 ps could be isolated from the dynamics of structurally specific marker bands of the BV chromophore. These results together with those of accompanying sub-picosecond Vis pump-Vis probe spectroscopy allow the extension of the reaction scheme for the primary process by a vibrationally excited electronic ground state. The isomerization at the C15=C16 bond occurs within the lifetime of the excited electronic state. A quantum yield of 0.094 for the primary reaction is determined, suggesting that the quantum yield of formation of the P(fr) far-red-absorbing form is already established in the primary photoreaction of the P(r) (red-absorbing) form.
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